Feature-Based Molecular Networking (FBMN) is a popular analysis approach for LC-MS/MS-based non-targeted metabolomics data. While processing LC-MS/MS data through FBMN is fairly streamlined, downstream data handling and statistical interrogation is often a key bottleneck. Especially, users new to statistical analysis struggle to effectively handle and analyze complex data matrices. In this protocol, we provide a comprehensive guide for the statistical analysis of FBMN results. We explain the data structure and principles of data clean-up and normalization, as well as uni- and multivariate statistical analysis of FBMN results. We provide explanations and code in two scripting languages (R and Python) as well as the QIIME2 framework for all protocol steps, from data clean-up to statistical analysis. Additionally, the protocol is accompanied by a web application with a graphical user interface (https://fbmn-statsguide.gnps2.org/), to lower the barrier of entry for new users. Together, the protocol, code, and web app provide a complete guide and toolbox for FBMN data integration, clean-up, and advanced statistical analysis, enabling new users to uncover molecular insights from their non-targeted metabolomics data. Our protocol is tailored for the seamless analysis of FBMN results from Global Natural Products Social Molecular Networking (GNPS and GNPS2) and can be adapted to other MS feature detection, annotation, and networking tools.

Dacryodes Vahl. species, belonging to the Burseraceae family, are widely used in traditional medicine in tropical regions to treat a range of ailments including malaria, wounds, tonsillitis, and ringworms. This review discusses the distribution, ethnobotanical uses, phytochemistry, and bioactivities of Dacryodes species. The intent is to spur future research into isolating and identifying key active principles, secondary metabolites, and crude extracts, and evaluating their pharmacological and toxicological effects, as well as the mechanism of actions to understand their medicinal benefits. A systematic review of scientific electronic databases from 1963 to 2022 including Scifinder, Scopus, Pubmed, Springer Link, ResearchGate, Ethnobotany Research and Applications, Google Scholar, and ScienceDirect was conducted with a focus on Dacryodes edulis (G.Don) H.J. Lam and Dacryodes rostrata (Blume) H.J. Lam. Pharmacological data revealed that D. edulis isolates contain secondary metabolites and other phytochemical groups belonging to the terpenoids class with anti-microbial, anticancer, antidiabetic, antiinflammatory and hepatoprotective activities, highlighting its pharmacological potential in the therapy or management of diverse cancers, cardiovascular, and neurological diseases. Thus, phytochemicals and standardized extracts from D. edulis could offer safer and cost-effective chemopreventive and chemotherapeutic health benefits/regimen, or as alternative therapeutic remedy for several human diseases. Nevertheless, the therapeutic potential of most of the plants in the genus have not been exhaustively explored with regard to phytochemistry and pharmacology, but mostly complementary approaches lacking rigorous, scientific research-based knowledge. Therefore, the therapeutic potentials of the Dacryodes genus remain largely untapped, and comprehensive research is necessary to fully harness their medicinal properties.

While anthropogenic pollution is a major threat to aquatic ecosystem health, our knowledge of the presence of xenobiotics in coastal Dissolved Organic Matter (DOM) is still relatively poor. This is especially true for water bodies in the Global South with limited information gained mostly from targeted studies that rely on comparison with authentic standards. In recent years, non-targeted tandem mass spectrometry has emerged as a powerful tool to collectively detect and identify pollutants and biogenic DOM components in the environment, but this approach has yet to be widely utilized for monitoring ecologically important aquatic systems. In this study we compared the DOM composition of Algoa Bay, Eastern Cape, South Africa, and its two estuaries. The Swartkops Estuary is highly urbanized and severely impacted by anthropogenic pollution, while the Sundays Estuary is impacted by commercial agriculture in its catchment. We employed solid-phase extraction followed by liquid chromatography tandem mass spectrometry to annotate more than 200 pharmaceuticals, pesticides, urban xenobiotics, and natural products based on spectral matching. The identification with authentic standards confirmed the presence of methamphetamine, carbamazepine, sulfamethoxazole, N-acetylsulfamethoxazole, imazapyr, caffeine and hexa(methoxymethyl)melamine, and allowed semi-quantitative estimations for annotated xenobiotics. The Swartkops Estuary DOM composition was strongly impacted by features annotated as urban pollutants including pharmaceuticals such as melamines and antiretrovirals. By contrast, the Sundays Estuary exhibited significant enrichment of molecules annotated as agrochemicals widely used in the citrus farming industry, with predicted concentrations for some of them exceeding predicted no-effect concentrations. This study provides new insight into anthropogenic impact on the Algoa Bay system and demonstrates the utility of non-targeted tandem mass spectrometry as a sensitive tool for assessing the health of ecologically important coastal ecosystems and will serve as a valuable foundation for strategizing long-term monitoring efforts.

Understanding how gut microbes transform drugs, and how this influences microbiome composition and function, remains a key question to better understand the efficacy and side effects of pharmaceuticals. To accelerate the discovery of microbiome-derived drug metabolites, we developed a functional metabolomics workflow that combines the use of synthetic microbial communities (SynComs) with a time-series resolved molecular networking approach and advanced computational metabolite annotation. We demonstrate how this framework can be used to illuminate chemical transformation dynamics in a gut SynCom (Com20) with 50 clinical drugs. Our results highlight a multitude of drug metabolites, including multi-step metabolic cascades, some of which correlated to shifts in microbial taxa, suggesting functional links between microbiome composition and biochemical transformations. Our computational data analysis workflow is publicly available through the GNPS2 ecosystem at chemprop.gnps2.org, which can be used to prioritize biotransformations and other (bio)chemical reactions in various biological and abiotic systems.

Canarium schweinfurthii, also called ‘’Elemierd’Afrique’’, is used in Cameroonian folk medicine (bark decoction) to treat patients suffering from hypertension. Aim of the study: This study aimed at evaluating the antihypertensive activities of the stem bark of Canarium schweinfurthii and identifying potential compounds present in its extract that may support or oppose its ethnomedicinial use. Stem bark extract of Canarium schweinfurthii was prepared by maceration using 70 % ethanol followed by redissolution in methanol and hyphenated. Ultra-Performance Liquid Chromatography-Tandem Mass Spectrometry (UPLC-MS/MS) analysis for the detection and characterisation of secondary metabolites. Antihypertensive effects were assessed in Wistar rats after induction of hypertension with sodium chloride (NaCl) 18 % at a dose of 0.01mL/g_{body weight} once a day for four weeks.Hemodynamic parameters were measured weekly by anon-invasive method using the CODA system. The ethanolic bark extract of C. schweinfurthii significantly inhibited the increase of blood pressure with a maximum of 23.18 % (systolic pressure, p < 0.0001), 24.77 % (diastolic pressure, p < 0.001) and 22.95 % (mean pressure, p < 0.0001) at a dose of 200 mg/kg_{body weight} at the 4th week, compared to agroup of Wistar rats that received only NaCl (negative control). Similarly, the extract significantly inhibited the increase in heart rate by 18.84 % (p < 0.001) at 200 mg/kg_{body weight} at week four. Hematological parameters did not differ significantly between the extract-treated and control groups. The UPLC-MS/MS spectrometric analysis provided evidence for the presence of several C30 terpenoids containing three or five oxygen atoms and exhibiting pentacyclic triterpenoid structures, as well as C29 terpenoids and related compounds containing nitrogen in addition to oxygen, using spectral matching, and in silico molecular formula and structure prediction. Additionally, two features were annotated with high-confidence as lignans, structurally closely related to hinokinin and dehydrocubebin through MS/MS-based in silico structure prediction using CSI: Finger ID in SIRIUS5. The lignans have been previously reported from stem bark of plants belonging to the Burseraceae family. Conclusion: The ethanolic stem bark extract of C. schweinfurthii demonstrated antihypertensive properties on the tested Wistar rats. These results support the ethnopharmacological use of C. schweinfurthii concoctions for the treatment of hypertension and suggest a protective effect against salt damage, hypothetically by the up regulation of antioxidative enzymes and/or lipids, mitigatings membrane peroxidation.